\section{NFcore::TransformationFactory Class Reference}
\label{classNFcore_1_1TransformationFactory}\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}}
{\tt \#include $<$transformation.hh$>$}

\subsection*{Static Public Member Functions}
\begin{CompactItemize}
\item 
static {\bf Transformation} $\ast$ {\bf genStateChangeTransform} (unsigned int cIndex, int newValue)
\item 
static {\bf Transformation} $\ast$ {\bf genBindingTransform1} (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genBindingSeparateComplexTransform1} (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genBindingTransform2} (unsigned int bSiteIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genUnbindingTransform} (unsigned int bSiteIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genAddMoleculeTransform} ({\bf SpeciesCreator} $\ast$sc)
\item 
static {\bf Transformation} $\ast$ {\bf genRemoveMoleculeTransform} ()
\item 
static {\bf Transformation} $\ast$ {\bf genEmptyTransform} ()
\item 
static {\bf Transformation} $\ast$ {\bf genIncrementStateTransform} (unsigned int cIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genDecrementStateTransform} (unsigned int cIndex)
\item 
static {\bf Transformation} $\ast$ {\bf genLocalFunctionReference} (string PointerName, int type, {\bf TemplateMolecule} $\ast$tm)
\end{CompactItemize}
\subsection*{Static Public Attributes}
\begin{CompactItemize}
\item 
static const unsigned int {\bf STATE\_\-CHANGE} = 0
\item 
static const unsigned int {\bf BINDING} = 1
\item 
static const unsigned int {\bf UNBINDING} = 2
\item 
static const unsigned int {\bf REMOVE} = 3
\item 
static const unsigned int {\bf ADD} = 4
\item 
static const unsigned int {\bf EMPTY} = 5
\item 
static const unsigned int {\bf INCREMENT\_\-STATE} = 6
\item 
static const unsigned int {\bf DECREMENT\_\-STATE} = 7
\item 
static const unsigned int {\bf LOCAL\_\-FUNCTION\_\-REFERENCE} = 8
\end{CompactItemize}


\subsection{Member Function Documentation}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genStateChangeTransform@{genStateChangeTransform}}
\index{genStateChangeTransform@{genStateChangeTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genStateChangeTransform (unsigned int {\em cIndex}, int {\em newValue})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_c8a9523b24c856ab84f106a8740d2baf}


Generates a state change \doxyref{Transformation}{p.}{classNFcore_1_1Transformation} for transforming the given state at the given index into the new state value. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genBindingTransform1@{genBindingTransform1}}
\index{genBindingTransform1@{genBindingTransform1}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genBindingTransform1 (unsigned int {\em bSiteIndex}, unsigned int {\em otherReactantIndex}, unsigned int {\em otherMappingIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_b43cb8fbbaa03e4edd9366bc922f9c2c}


Generates a binding transformation for one of the two binding sites in the binding Transform. You will have to tell it where the other \doxyref{Transformation}{p.}{classNFcore_1_1Transformation} object lives (\doxyref{TransformationSet}{p.}{classNFcore_1_1TransformationSet} has this information). \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genBindingSeparateComplexTransform1@{genBindingSeparateComplexTransform1}}
\index{genBindingSeparateComplexTransform1@{genBindingSeparateComplexTransform1}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genBindingSeparateComplexTransform1 (unsigned int {\em bSiteIndex}, unsigned int {\em otherReactantIndex}, unsigned int {\em otherMappingIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_275722d56c36dfe9be8e8cca8fcc4fab}


\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genBindingTransform2@{genBindingTransform2}}
\index{genBindingTransform2@{genBindingTransform2}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genBindingTransform2 (unsigned int {\em bSiteIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_60536e9fb733aa835613410f1cf3ec25}


Generates the second half of a binding transform. The other site already knows about this site, so all you need here is the index of the binding site that must be bonded. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genUnbindingTransform@{genUnbindingTransform}}
\index{genUnbindingTransform@{genUnbindingTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genUnbindingTransform (unsigned int {\em bSiteIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_6d0b9445e9c48c59f807c727445054ab}


Generates an unbinding transformation for a particular binding site. Only one of the binding sites must be specified as a \doxyref{Transformation}{p.}{classNFcore_1_1Transformation} - the other is automatically taken care of. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genAddMoleculeTransform@{genAddMoleculeTransform}}
\index{genAddMoleculeTransform@{genAddMoleculeTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genAddMoleculeTransform ({\bf SpeciesCreator} $\ast$ {\em sc})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_f11322a3ba45cabe38b2eadf032a1ff6}


Generates an Add \doxyref{Molecule}{p.}{classNFcore_1_1Molecule} transformation. Currently, this is not yet implemented. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genRemoveMoleculeTransform@{genRemoveMoleculeTransform}}
\index{genRemoveMoleculeTransform@{genRemoveMoleculeTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genRemoveMoleculeTransform ()\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_5d848169fa346fc9642cc34ecf706ea3}


Generates a removal of a molecule from the system. Currently this is not yet implemented. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genEmptyTransform@{genEmptyTransform}}
\index{genEmptyTransform@{genEmptyTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genEmptyTransform ()\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_4bcd9f929fb6c17f6935dea191e9e9aa}


Generates an empty transformation. This is used in cases where there is a reactant that is not transformed in a reaction, but that still needs to be counted and marked so that the rate of the reaction is correct. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genIncrementStateTransform@{genIncrementStateTransform}}
\index{genIncrementStateTransform@{genIncrementStateTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genIncrementStateTransform (unsigned int {\em cIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_250f200fbcc8e794b8b99cc45302ab3b}


Generates an IncrementState transformation. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genDecrementStateTransform@{genDecrementStateTransform}}
\index{genDecrementStateTransform@{genDecrementStateTransform}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf NFcore::Transformation} $\ast$ TransformationFactory::genDecrementStateTransform (unsigned int {\em cIndex})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_eece84f71547208fa9e27ecda1032489}


Generates an DecrementState transformation. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!genLocalFunctionReference@{genLocalFunctionReference}}
\index{genLocalFunctionReference@{genLocalFunctionReference}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}{\bf Transformation} $\ast$ TransformationFactory::genLocalFunctionReference (string {\em PointerName}, int {\em type}, {\bf TemplateMolecule} $\ast$ {\em tm})\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_206a59330bba84e1b0131b8b0ba919f4}




\subsection{Member Data Documentation}
\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!STATE\_\-CHANGE@{STATE\_\-CHANGE}}
\index{STATE\_\-CHANGE@{STATE\_\-CHANGE}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::STATE\_\-CHANGE} = 0\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_5b83f8ccba33c9c11d57ccb01eb65b8b}


Indicates a state change transformation or mapping onto a state \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!BINDING@{BINDING}}
\index{BINDING@{BINDING}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::BINDING} = 1\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_9d39c00ef66f1a76c2d0d466753382e6}


Indicates a binding transformation or mapping onto a binding site \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!UNBINDING@{UNBINDING}}
\index{UNBINDING@{UNBINDING}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::UNBINDING} = 2\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_b7940a37633cc5c84bb5d8e7181cda04}


Indicates an unbinding transformation or mapping onto a binding site \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!REMOVE@{REMOVE}}
\index{REMOVE@{REMOVE}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::REMOVE} = 3\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_5a5169186f10927cf62a9a542d1b1b95}


Indicates a removal transform or mapping onto an entire \doxyref{Molecule}{p.}{classNFcore_1_1Molecule} \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!ADD@{ADD}}
\index{ADD@{ADD}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::ADD} = 4\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_492322bf2daa6a96dca1bb1b13d7a1d5}


Indicates an addition transform \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!EMPTY@{EMPTY}}
\index{EMPTY@{EMPTY}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::EMPTY} = 5\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_6248b102fcc6990bfbca65d3dfa4764e}


Indicates no transformation is needed (or is the second partner in a binding transform and so should be skipped when applying transforms \index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!INCREMENT\_\-STATE@{INCREMENT\_\-STATE}}
\index{INCREMENT\_\-STATE@{INCREMENT\_\-STATE}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::INCREMENT\_\-STATE} = 6\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_bb9132a59d041a40b6503fffc37e51c5}


\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!DECREMENT\_\-STATE@{DECREMENT\_\-STATE}}
\index{DECREMENT\_\-STATE@{DECREMENT\_\-STATE}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::DECREMENT\_\-STATE} = 7\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_ef1bf254664f1baaa23127355a427fde}


\index{NFcore::TransformationFactory@{NFcore::TransformationFactory}!LOCAL\_\-FUNCTION\_\-REFERENCE@{LOCAL\_\-FUNCTION\_\-REFERENCE}}
\index{LOCAL\_\-FUNCTION\_\-REFERENCE@{LOCAL\_\-FUNCTION\_\-REFERENCE}!NFcore::TransformationFactory@{NFcore::TransformationFactory}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}const unsigned int {\bf NFcore::TransformationFactory::LOCAL\_\-FUNCTION\_\-REFERENCE} = 8\hspace{0.3cm}{\tt  [static]}}\label{classNFcore_1_1TransformationFactory_2082f8fc11ff7315d0454c2bf61bf0e4}




The documentation for this class was generated from the following files:\begin{CompactItemize}
\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFreactions/transformations/{\bf transformation.hh}\item 
/home/msneddon/eclipse/ganymede\_\-cpp/workspace/NFsim\_\-svn/src/NFreactions/transformations/{\bf transformation.cpp}\end{CompactItemize}
